SRNAs) showed the highest methylation levels in males (Figure S3D). Given that degenerating testis tissue

SRNAs) showed the highest methylation levels in males (Figure S3D). Given that degenerating testis tissue and stored sperm account for any significant fraction of body weight in male ants, this observation suggests that rasRNAs target preferentially active transposons inside the male germline. DNA methylation peaks in the begin from the second exon Inside the body on the typical ant gene, methylation increased sharply at the ATG and decreased within the 3 direction, returning to background levels at the quit codon (Figure 2C, S4A). This pattern was practically identical across castes and developmental stages and in between the two species. DNA methylation peaked 750 bp downstream of your ATG (Figure S4B), which corresponds to the get started from the second exon of methylated genes (Figure S4C). In contrast, the typical commence of the second exon when all genes were considered–HHMI Author Manuscript HHMI Author Manuscript HHMI Author ManuscriptCurr Biol. Author manuscript; obtainable in PMC 2013 April 09.Bonasio et al.Pageregardless of their methylation status–was at +1,475 bp (Camponotus) and +1,525 bp (Harpegnathos). In reality, the typical intron size involving methylated and unmethylated genes varied significantly, and this difference was also observed inside a. mellifera, but not B. mori (Figure S4C).HHMI Author Manuscript HHMI Author Manuscript HHMI Author ManuscriptWithin the gene physique, mCs accumulated on exons (Figure 2D, S4D), and were largely absent from introns, as observed in other organisms [23]. We reanalyzed genome-wide DNA methylation information to get a. mellifera [14] (Figure S4E) and B. mori [10] and identified similar patterns, even though within the latter introns contained detectable amounts of DNA methylation (Figure S4F). The higher mC density in exons in comparison with introns in ants and other organisms suggests a link between DNA methylation and the transcription/splicing machinery (see below). Connection between caste-specific methylomes and transcriptomes To compare DNA methylation and gene expression, we utilized our published RNA-seq datasets [4] and integrated them with newly generated datasets for mature queens and virgin queens. Genome-wide, methylation levels exhibited for essentially the most aspect a constructive correlation with RNA levels, except for probably the most highly expressed genes (Figure 3A ), as originally located in plants as well as other organisms [19, 24]. Methylated genes exhibited lower sample MedChemExpress GW 485801 specificity [25] than unmethylated genes (Figure 3C ), which suggests that they’re enriched for constitutively expressed housekeeping genes, which contribute RNA and methylated genomic DNA from all tissues and are for that reason much more represented in whole-body samples. This is consistent with predictions based on genome-wide patterns of CpG depletion in a. mellifera [26]. At the single gene level, the correlation among methylation and RNA levels was not as striking as it was genome-wide (Figure 3E ), which might clarify why the unsupervised hierarchical clustering of embryos, larvae, and adult castes as outlined by their expression or methylome profiles yielded trees with distinct topologies (Figure S5). In Camponotus, the methylome profile drew the clearest distinction amongst sexual castes plus the remaining samples (Figure S5A), whereas at the transcriptome level the hugely reproductive queen was drastically distinct in the other adult castes (Figure S5B). In Harpegnathos, the DNA methylation profiles of gamergates and workers were a lot more similar PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/21178946 than their transcriptomes (Figure S5C ), suggesting that not.